Welcome, @gozdekb
This is a prior post with some help → nf-core Pipeline Integration to Local Galaxy
This part is probably a clue. If Planemo works, but working directly on your server doesn’t – maybe look for the difference at that part? Meaning, did your Galaxy installation get set up correctly? Do datasets load? Do the default tools in the tool panel execute? Is there anything reported in the server logs?
Let’s start there, thanks! 